Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

can´t open an image in Freeview
by Adam Rytina 18 Oct '19

18 Oct '19

External Email - Use Caution Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue? Thanks a lot Adam [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-anima…]<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Bez virů. www.avast.com<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…>

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Post-doc on multi-tracer PET-MRI
by Linnman, Clas,Ph.D. 18 Oct '19

18 Oct '19

Hi everyone, My lab is looking for a post-doc. Please spread the below advertisement far and wide With my best regards Clas Linnman The Spaulding Neuroimaging Laboratory (PI Clas Linnman, assistant professor, Harvard Medical School), working closely with the Martinos Center for Biomedical Imaging, uses simultaneous PET-MRI with a focus on neuroinflammation and opioid receptors in humans and in animal models of chronic pain. The current position is part of a research project funded by the NIH to determine if intensive aerobic exercise may reduce inflammation, strengthen endogenous pain capacity, and improve rehabilitation outcomes in patients with spinal cord injury. Key Responsibilities Conduct neuroimaging research with emphasis on brain structure, network reorganization, opioid receptor expression and neuroinflammation after spinal cord injury. Evaluate the effects of intensive whole-body aerobic exercise in patients with sub-acute spinal cord injury with regards to pain inhibition capacity, spinal cord atrophy, brain function, opioid and neuroinflammation. Apply and develop MR and PET acquisition methods for longitudinal analyses Apply and develop research methodologies for integrating PET and MR data in human and animal models. Lead and assist in the writing of academic manuscripts Lead and assist in dissemination of research findings through presentations at conferences and for patient and public engagement activities. Initiate and assist grant applications for further career development Assist in mentoring of research assistants Qualifications Qualifications and Experience Education/Degree Required - A PhD degree in a field encompassing neuroscience and neuroimaging. Experience Preferred Research experience in neuroscience and neuroimaging; preferably in the fields of pain, SCI and MR data analysis, as demonstrated by at least one first-author publication for which MRI or PET methodology has been used. Candidates are expected to have considerable experience in the analysis of neuroimaging data, basic programming skills in Python or Matlab, and a solid understanding of inferential statistics. Excellent organizational, oral, and written communication skills Strong interpersonal skills and comfort interacting with research participants with spinal cord injuries English language fluency Excellent ability to work independently Familiarity with neuroimaging tools like Freesurfer, SPM, FSL Excellent attention to detail Apply online at https://partners.taleo.net/careersection/srn/jobdetail.ftl?job=3108990&tz=G…

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Research Specialist Position at the Center for Healthy Minds
by CHM Recruiting 18 Oct '19

18 Oct '19

External Email - Use Caution The Center for Healthy Minds at the University of Wisconsin-Madison is hiring a Research Specialist! To learn more about this excellent job opportunity, please view the attached Position Description. Thank you, Center for Healthy Minds

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Group effect Contrast for 6 groups
by cody samth 18 Oct '19

18 Oct '19

External Email - Use Caution Hi, I'm designing an analysis that will have 6 groups (two factors/three levels). I was wondering if I could get some input regarding my contrast for the group effect. Based on the group effect contrast under the FSGD examples for 3 groups I've written a five line contrast file that compares group 1 against the other 5 groups. 1-1 0 0 0 0 1 0 -1 0 0 0 1 0 0 -1 0 0 1 0 0 0 -1 0 1 0 0 0 0 -1 Which from my understanding should cover the rest of the contrasts such as 2v5 3v6 and etc. Is my understanding of this correct?

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Mri_mask producing only zeros
by Sims, Sara A (Campus) 18 Oct '19

18 Oct '19

External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then into a surface with 1s inside the label and 0s outside the label. I want to make a connectivity map surface overlay with values only within my label overlay. However when I run it, it creates a surface overlay with only zeros. There is definitely values within the label surface overlay (I triple checked). Code I used: Mri_mask original_surface_overlay label_mask new_masked_output It doesn’t output any errors. Sara A. Sims

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-multistrip exited with errors troubleshooting
by Mohn, Johannes 18 Oct '19

18 Oct '19

External Email - Use Caution Hi all, I'm trying -multistrip to improve skull stripping for subjects where incomplete skull strip lead to inaccurate pial surfaces. The command I'm running is: recon-all -multistrip -clean-bm -s <subjID> -no-isrunning However, multistrip fails. It exits with errors and no new brainmask.mgz files are created. This is independent of the subject. It fails for all. I attached the recon-all.log for one exemplary subject. In contrast, using -gcut (recon-all -skullstrip -clean-bm -gcut -s <subjID>) works but does not remove the problematic skull fragments in most cases. Independent of whether -multistrip or -gcut are better suited to improve the skull stripping, I would like to understand why -multistrip fails in my case and what can be done to make it work. Best, JJ

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brain mask without CSF ...
by stefano.silvoni＠libero.it 18 Oct '19

18 Oct '19

External Email - Use Caution Dear FreeSurfer Experts, I am running a functional analysis of subcortical structures using FS-FAST (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a brain mask excluding CSF; would it be possible using some option/flag in 'preproc-sess'? or should I do it manually? maybe using a command like that? mri_binarize --i $sbjdir/mri/aparc.a2009s+aseg.mgz --match 702 703 --o $sbjdir/mri/GM-WM_mask.mgz because I saw in FreeSurferColorLUT.txt the following definitions: 702 GrayMatter-FSL-FAST 205 62 78 0 703 WhiteMatter-FSL-FAST 0 225 0 0 or is there another strategy? thanks in advance best stefano silvoni

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covariate with repeated anova
by miracle ozzoude 18 Oct '19

18 Oct '19

External Email - Use Caution Hello Experts, I would like to include covariates in the freesurfer repeated anova steps https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. When i tried including 3 covariates, mri_glmfit complained about "martix is ill-conditioned". How do i fix it? Below is an example my fsgd file. I've also attached the matrix design in the email. GroupDescriptorFile 1 Class PsyDis1 Class PsyDis2 Variables TP1vsTP2 Age Llesion Rlesion Input Psy1_Pre.long.Psy1 PsyDis1 1 68 96 61 Input Psy1_6mos.long.Psy1 PsyDis1 -1 68 96 61 Input Psy2_Pre.long.Psy2 PsyDis2 1 39 217 140 Input Psy2_6mos.long.Psy2 PsyDis2 -1 39 217 140 contrast: 0 0 1 0 0 Best, Paul

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Re: [Freesurfer] Download link broken
by Hoopes, Andrew 18 Oct '19

18 Oct '19

Hi Tashrif, sorry, we had a network outage last night, but the link should be fixed now. best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Billah, Tashrif" <tbillah(a)bwh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, October 18, 2019 at 10:08 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Download link broken Hi FreeSurfer team, The following link appears broken since 10/17 evening. https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin… Can you look into it? Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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Download link broken
by Billah, Tashrif 18 Oct '19

18 Oct '19

Hi FreeSurfer team, The following link appears broken since 10/17 evening. https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin… Can you look into it? Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS<https://www.linkedin.com/in/tashrif-billah/> Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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